This guide records the original experiments behind the direct annotations. Existing publication excerpts are preserved verbatim; their presence does not expand the assay scope. The three natural human products (592, 559 and 557 residues) are distinct. A human host, an accession label or a shared-peptide identification does not establish that every product was tested.
| Original | Operative public locator | Evidence and limits |
|---|---|---|
| 19234442 | Main Results; Figures 2 and 4; Methods, immunoprecipitation and in vitro phosphatase assay | Actual Methods/Results and Figure 2/4 pixels inspected. HA-Eya1 isolates dephosphorylate H2AX, with D323A comparison; endogenous human EYA1 knockdown changes H2AX phosphorylation. Tagged Eya1 localizes at irradiated nuclear foci. Bacterial pSer-H2AX comparison is Eya3 residues 240–573, not EYA1. I-PpoI ChIP, S219 mutation and MDC1 experiments are Eya3-specific. Eya1 rescue is reported for a supplement that was not inspected. |
| 27795300 | Results, Figures 1–3 and 8 captions; construct, affinity purification and peptide-assay Methods | FLAG-EYA1 preparations release phosphate from pThr58-Myc; endogenous human breast-cell perturbation changes Myc phosphorylation/stability. Preparation activity does not alone identify the catalyst; exact insert accession/species is absent from the inspected construct section. No figure pixels inspected. |
| 29535359 | Results/Figure 3; Figure 1/4 captions; expression, purification and phosphatase Methods; Discussion | Human EYA1 associates with PP2A-C and its FLAG isolate has pThr activity. The decisive PP2A dependence and purified reconstitution use mouse Eya3. The authors leave member/species differences open; no wholesale Eya3-to-EYA1 mechanism transfer. No figure pixels or supplement inspected. |
| 33472197 | Results/Figure 6 caption; protein-expression/purification and peptide Methods; Supplementary Figure S6, page 11 | Positive full-length Eya1 aPKC-pThr410 activity, catalytic-mutant comparison and B55alpha-negative active preparation are retained. Actual S6 pixels include positive DRG and SF9 lysate controls. The source alternates S2/Sf9 and D327A/D328A terminology and does not resolve the exact natural human construct. |
| 10490620 | Construct Methods; Figure 2; Table 1 | Mouse Eya1 and Six constructs in COS7 cells positively coactivate myogenin/Six-element reporters and show Six-dependent Eya1 nuclear translocation. Figure 2 pixels inspected. Native rat co-IP is Eya3/Six5; Eya2 domain work is not an Eya1 assay. |
| 15141091 | Methods; Eya1–Six1 interaction Results; Figure 4 | Mouse Six1 with Eya1-domain yeast prey and Eya1/Six1 reporter cooperation. Figure 4 pixels inspected. Eya1 insert species/accession is not specified in the inspected Methods; HEK293 host does not settle it. |
| 19497856 | Cell-fractionation Methods; Figure 5B caption/Results | Full-length FLAG-EYA1 fractionation in MCF7 cells establishes cytoplasmic EYA1 alone and nuclear EYA1 with compatible SIX1. The accession is unspecified. Purified binding/stoichiometry and reporter assays use EYA2. No figure pixels inspected. |
| 14628042 | Author-upload original, printed pages 250–253; Figure 6 caption and Methods | Actual web-rendered original read. Mouse Six1/Eya1 genetic interactions support organogenesis. Plotted peptide specificity and coactivator recruitment are Eya3, some Eya1 activities are reported without shown data, and the ChIP antibody recognizes Eya1/3. No figure pixels/supplement inspected. |
| 12500905 | Verified abstract and publisher preview | Human embryo expression, with mainly cytoplasmic Eya1/Eya2. Complete original Methods/Results unavailable. Nuclear biology is independently established; its precise assay is not represented as inspected. |
| 9020840 | Verified abstract and publisher preview | Human BOR genetics and murine ear/kidney expression. Complete original Methods/Results unavailable. Neither a developmental-only role nor sensory-transduction participation is established by the accessible scope. |
The four direct binding contexts all name human SIX1, Q15475, an independently established DNA-binding transcription factor. GO:0140297 therefore specifies the partner class without inferring coactivation from an interaction screen alone.
BioPlex_interactionList_v2.tsv, row 5179, Q15475–Q99502; BioPlex_2.0_293T_DirectedEdges.tsv, rows 17120–17121, both orientations. Actual original Methods/Results and the full public tables were inspected. C-terminal HA-FLAG AP-MS in HEK293T establishes cellular association, not an isolated two-protein reaction.BioPlex_293T_Network_10K_Dec_2019.tsv, row 36249; directed rows 42548–42549. Actual original BioC main and public tables were inspected. No EYA1 record in the inspected HCT116 files is a dataset observation rather than a biological negative. The accession label and AP-MS protein grouping do not establish all-product equivalence.The 2009 minimal-pSer excerpt is an Eya3-fragment result, and the general SIX/EYA bipartite-factor sentence is background rather than an EYA1-specific reporter result. The 2003 phosphatase-switch excerpt includes Eya3-specific mechanistic work. These inherited texts remain unchanged but are explicitly contextualized in the revised reasons. No new publication quotations were added.
The positive H2AX step is a repair-regulatory mechanism; detailed Eya3 ChIP, rescue and recruitment assays are not relabeled EYA1. Cytoplasmic detection is positive evidence and does not establish an inactive storage pool. The broad morphogenesis assertion is refined to the already supported inner-ear morphogenesis role; precise sensory-perception participation remains unresolved because its operative source evidence was not recovered. The two existing NEW rows are historical assertions being reassessed, not additional annotations or a newly asserted coverage gap.
PMID:14628052(https://doi.org/10.1038/nature02093), actual author-original Results and Methods, tests bacterial mouse Eya1 domain residues 319–591. The plotted phosphopeptide specificity is Eya3-domain evidence, not a full-length EYA1 negative. No supplementary Table 2 or figure pixels were inspected.
The 2018 PP2A paper's correction changes the Figure 7 legend title from increased to decreased metastasis; it does not change the human EYA1 association experiment. For PMID:33472197, the database assessment also inspected the official supplementary Tables S1/S2 and Figure S6 caption, whereas the direct assessment independently read the main operative blocks and S6 pixels. These read scopes are separately identified in the shared reference assessment.
The current Human Protein Atlas EYA1 page assigns supported nucleoplasm and nuclear-body localization. Selected HPA028917 Rh30 and U2OS composites show diffuse/granular nuclear signal and brighter puncta; the selected RPE1 image is weaker. The 146-residue antigen is present in all three source products. The images do not establish isoform-specific localization, a particular nuclear-body subtype or a specialized nuclear-body mechanism. Broad nucleus and specific nucleoplasm annotations can coexist without requiring every observation to have the same spatial resolution.
In Reactome R-HSA-5683964, input set 5683966 hasMember EYA1 5683625; output set 5683980 hasCandidate phosphorylated EYA1 5683951. Both entities independently identify human Q99502 residues 1–592 and their own nucleoplasm compartment. EYA1 is the phosphorylation substrate of ATM in this event. The modeled location does not make EYA1 the event's kinase or resolve shorter products.
Actual PTHR10190 ancestry places human EYA1 leaf PTN002468887 below positive IBDs at PTN000022641 and PTN002565172. The ungapped target alignment matches the displayed 592-residue sequence exactly, and no target-path NOT was found. Self-WITH evidence is legitimate. The current differentiation IBD contains an additional zebrafish descendant absent from the imported WITH list; the version-specific records are retained separately.
The current H2AX-Y142 phosphatase term connects to chromatin remodeling through the typed path GO:0140793 is_a GO:0140789 is_a GO:0140993 part_of GO:0006338. This is not is_a subsumption of a molecular function by a biological process. Histone-state regulation therefore supports the process without asserting an ATP-driven EYA1 nucleosome motor. The inner-ear morphogenesis term concerns development of ear structures, not execution of hearing. PMID:10471511(https://pubmed.ncbi.nlm.nih.gov/10471511/) was available only as metadata and publisher abstract here; its mouse otic-vesicle arrest finding is positive context, but the operative developmental Methods/Results were not recovered. This limitation does not invalidate the independently inspected PAINT placement.
The mouse P97767 donor's current SUMO annotation points to PMID:16990542(https://doi.org/10.1126/science.1128406). The actual main text and supplementary Methods describe Myc-Eya1, HA-SUMO1 and UBC9 in 293T cells, followed by detection of conjugates on Eya1. The source numbering follows cited mouse Eya1 work; a human expression host is not a human-construct identifier. PMID:24954506(https://doi.org/10.1038/onc.2014.179) independently detects SUMO on endogenous human EYA1 and studies mouse Eya1 constructs with SENP2 and lysine-mutant controls. Its site interpretation favors K43/K146 rather than simply transferring the earlier K459 interpretation.
These are positive demonstrations of EYA1 regulation by SUMO. They do not demonstrate EYA1 executing the attachment step performed by UBC9 and the conjugation machinery. Removing the transferred protein-sumoylation process attribution therefore preserves the observed modification while correcting the assigned role.
The ordered coactivator core uses the original mouse Eya1/Six study, Methods (mouse cDNAs and COS7 reporters), Figures 2–3 and Table 1. The SIX1 mutation study, Methods and Figures 3–4, provides Eya1/Six1 interaction and reporter cooperation; its human HEK293 host does not establish the Eya1 insert's species or natural product. Human EYA1–SIX1 screen records independently support the conserved partnership. In the 2009 biochemical study, Figure 5B is the EYA1 nuclear-localization experiment, whereas the purified binding and reporter work is EYA2. The inherited bipartite-factor quotation is retained as family context. The inherited SIX1–DACH switch quotation also retains its position; the detailed coactivator-recruitment assays use Eya3 and do not prove a universal EYA1 switch.
The ordered phosphatase core uses H2AX damage-response experiments, Figures 2D and 4B–E and the in-vitro phosphatase/siRNA Methods. The Eya1 affinity isolate and endogenous human knockdown support H2AX phosphotyrosine regulation. The bacterially purified peptide assay, detailed I-PpoI/MDC1 work and plotted rescue are Eya3; the additional Eya1 rescue is reported in the main text but its supplement was not inspected. The retained broad EYA quotations therefore do not claim that every experiment individually tested EYA1. PMID:14628052(https://pubmed.ncbi.nlm.nih.gov/14628052/) provides the independently inspected mouse Eya1-domain tyrosine-phosphatase assay described above.
The core retains GO:0004725 and explicitly describes the H2AX reaction. The current classification of GO:0140793 reaches histone phosphatase and chromatin remodeling, but does not contain GO:0004725 in its captured ancestry. The two activities are not duplicated to conceal that classification boundary. Positive repair regulation remains distinct from the enzymes that restore DNA strands. The conserved inner-ear developmental assertion is retained independently of any untested otic promoter mechanism.
The Ser/Thr attribution question retains the positive preparation assays and the competing partner evidence: PMID:27795300(https://pmc.ncbi.nlm.nih.gov/articles/PMC5192086/), Figures 1–3 and Methods; PMID:29535359(https://pmc.ncbi.nlm.nih.gov/articles/PMC5849647/), Figure 3 versus the mouse Eya3 mechanistic experiments; and PMID:33472197(https://pmc.ncbi.nlm.nih.gov/articles/PMC8118085/), Figure 6, Figure S6 and protein-purification Methods. Figure S6 includes positive DRG/SF9 lysate controls. No new original or figure acquisition was needed for synthesis; the earlier direct/database read scopes and access limits remain authoritative.
GO:0042472 inner ear morphogenesis is an is_a descendant of anatomical structure morphogenesis. The inspected PTHR10190 family places exact human Q99502 at PTN002468887 below the positive GO:0042472 IBD at PTN002565172. That ancestral judgment and conserved developmental evidence support this refinement of the broader existing assertion. GO_REF:0000033 describes the method, while the actual tree/MSA/IBD establishes the target placement. The unrelated bare repair citation PMID:19234442 was removed from this developmental row; inherited ear/kidney excerpts remain unchanged historical context. Metanephros development is a separate developmental context and is not included in that replacement. The unresolved sound-perception row makes no negative functional judgment: the full original experiments behind its precise TAS assertion remain unavailable.
GO:2000781 positive regulation of double-strand break repair retains the irradiation/DSB specificity of the existing repair context while describing the demonstrated H2AX-regulatory step. It replaces broad positive repair regulation in the ordered second core; the general accepted regulatory assertions are entailed. It does not assign ligation or completed-break-repair kinetics to EYA1, and Eya3-specific I-PpoI, MDC1 and plotted-rescue experiments remain separate.
The existing PMID:19351884 original was inspected directly: Methods use human EYA2 residues 268–538 and EYA3 residues 255–536 expressed in E. coli; Figures 2–3/Results measure those domains and EYA3 depletion in U2OS. The Discussion leaves other EYA proteins’ cellular roles open. This is not an EYA1-negative experiment. It provides family-mechanism context, while PMID:19234442(https://pmc.ncbi.nlm.nih.gov/articles/PMC2692521/) supplies the Eya1-isolate and endogenous human EYA1 evidence. No new figure pixels or supplementary assays were inspected for this clarification.
The broad protein-tyrosine-phosphatase core remains deliberate. Fresh official is_a closure still does not place the H2AX-specific term beneath GO:0004725. Its reaction is stated explicitly in the core; the independently measured Eya1-domain phosphatase and histone-substrate roles are not duplicated into separate cores.
The summary now includes the N-terminal activation/C-terminal Eya architecture, SIX-mediated DNA recognition, conserved developmental roles, and SUMO/Akt regulation. The curated Q99502 record supplies the retained developmental/disease context, including otofaciocervical syndrome; its similarity-based roles are not relabeled as human experimental assays. The conserved SIX2/SIX4/SIX5 cooperation comes from the actual mouse Eya1 study above. The detailed Eya3 SIX1–DACH switch is not presented as a universally demonstrated EYA1 mechanism. Precise GDNF ordering and cataract/anterior-segment mechanisms were not newly asserted from uninspected evidence.
For SUMO/Akt, PMID:24954506(https://pmc.ncbi.nlm.nih.gov/articles/PMC4275428/) Results/Figures 1–3 and the expression, kinase and reporter Methods distinguish endogenous human EYA1–SUMO/Akt observations from mouse Eya1 constructs in HEK293. The reporter/kinase experiments support SUMO restraint and Akt-dependent enhancement in that conserved system, without mapping mouse S298/K43/K146 coordinates onto every natural human product. EYA1 remains the SUMO substrate, not the conjugating enzyme.
All 60 inherited supporting-text values, ordered paths and reference associations remain exact. In particular, the first quotation on the inherited coactivator NEW row is localization context; the actual mouse Eya1/Six reporters provide the coactivation evidence. It was not deleted, moved or replaced with a new quotation. The two NEW rows are inherited assertions; no additional annotation is proposed in this bounded revision. Administrative lane labels are removed from reference assessments while actual assay, species/product and access limits remain documented.